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1. Natural allelic variations ofSaccharomyces cerevisiaeimpact stuck fermentation due to the combined effect of ethanol and temperature; a QTL-mapping study

Author

Margaux Bernard, Chantal Mansour, Pascal Durrens, Philippe Marullo, Emilien Peltier, and Denis Dubourdieu

Subjects
education.field_of_study, Population, Saccharomyces cerevisiae, food and beverages, Ethanol fermentation, Biology, Quantitative trait locus, biology.organism_classification, Yeast, Stuck fermentation, Fermentation, Food science, education, Winemaking
Abstract

BackgroundFermentation completion is a major prerequisite in many industrial processes involving the bakery yeastSaccharomyces cerevisiae.Stuck fermentations can be due to the combination of many environmental stresses. Among them high temperature and ethanol content are particularly deleterious especially in bioethanol and red wine production. Although the genetic causes of temperature and/or ethanol tolerance were widely investigated in laboratory conditions, few studies investigated natural genetic variations related to stuck fermentations in high gravity matrixes.ResultsIn this study, three QTLs linked to stuck fermentation in winemaking conditions were identified by using a selective genotyping strategy carried out on a backcrossed population. The precision of mapping allows the identification of two causative genesVHS1andOYE2characterized by stop-codon insertion. The phenotypic effect of these allelic variations was validated by Reciprocal Hemyzygous Assay in high gravity fermentations (>240 g/L of sugar) carried out at high temperatures (>28°C). Phenotypes impacted were related to the late stage of alcoholic fermentation during the stationary growth phase of yeast.ConclusionsThe genes identified are related to molecular functions such as Programed Cell Death, ROS metabolism and respire-fermentative switch and were never related to fermentation efficiency. Our findings open new avenues for better understanding yeast resistance mechanisms involved in high gravity fermentations.

Published
2019
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2. Molecular typing of wine yeast strains Saccharomyces bayanus var. uvarum using microsatellite markers

Author

Pascal Durrens, Marc Lollier, Isabelle Masneuf-Pomarède, C. Le Jeune, Michel Aigle, and Denis Dubourdieu

Subjects
Electrophoresis, Saccharomyces cerevisiae, Saccharomyces bayanus, Wine, Locus (genetics), Applied Microbiology and Biotechnology, Microbiology, Saccharomyces, 03 medical and health sciences, Typing, Mycological Typing Techniques, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, Winemaking, Genetics, 0303 health sciences, biology, Chimera, 030306 microbiology, biology.organism_classification, Yeast in winemaking, Karyotyping, Microsatellite, Genome, Fungal, Microsatellite Repeats
Abstract

The Saccharomyces bayanus var. uvarum yeasts are associated with spontaneous fermentation of must. Some strains were shown to be enological yeasts of interest in different winemaking processes. The molecular typing of S. bayanus var. uvarum at the strain level has become significant for wine microbiologists. Four microsatellite loci were defined from the exploration of genomic DNA sequence of S. bayanus var. uvarum. The 40 strains studied were homozygote for the locus considered. The discriminating capacity of the microsatellite method was found to be equal to that of karyotypes analysis. Links between 37 indigenous strains with the same geographic origin could be established through the analysis of microsatellite patterns. The analysis of microsatellite polymorphism is a reliable method for wine S. bayanus var. uvarum strains and their hybrids with Saccharomyces cerevisiae identification in taxonomic, ecological studies and winemaking applications.

Published
2007
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3. Saccharomyces forkhead protein Fkh1 regulates donor preference during mating-type switching through the recombination enhancer

Author

Eric Coïc, Pascal Durrens, Zhiqi Zhou, James E. Haber, and Kaiming Sun

Subjects
Saccharomyces cerevisiae Proteins, Genes, Fungal, Molecular Sequence Data, Saccharomyces cerevisiae, Cell Cycle Proteins, Locus (genetics), Saccharomyces, Open Reading Frames, Forkhead Transcription Factors, Species Specificity, Sequence Homology, Nucleic Acid, Two-Hybrid System Techniques, Genetics, Gene conversion, Enhancer, Alleles, Recombination, Genetic, Binding Sites, Base Sequence, Models, Genetic, biology, fungi, DNA, Genes, Mating Type, Fungal, biology.organism_classification, Precipitin Tests, Chromatin, Open reading frame, Mating of yeast, Mutation, Gene Deletion, Research Paper, Transcription Factors, Developmental Biology
Abstract

Saccharomyces mating-type switching results from replacement by gene conversion of the MAT locus with sequences copied from one of two unexpressed donor loci, HML or HMR. MATa cells recombine with HMLα ∼90% of the time, whereas MATα cells choose HMRa 80%–90% of the time. HML preference in MATa is controlled by the cis-acting recombination enhancer (RE) that regulates recombination along the entire left arm of chromosome III. Comparison of RE sequences between S. cerevisiae, S. carlsbergensis, and S. bayanus defines four highly conserved regions (A, B, C, and D) within a 270-bp minimum RE. An adjacent E region enhances RE activity. Multimers of region A, D, or E are sufficient to promote selective use of HML. Regions A, D, and E each bind in vivo the transcription activator forkhead proteins Fkh1p and Fkh2p and their associated Ndd1p, although there are no adjacent open reading frames (ORFs). Deletion of FKH1significantly reduces MATa's use of HML, as does mutation of the Fkh1/Fkh2-binding sites in a multimer of region A. We conclude that Fkh1p regulates MATa donor preference through direct interaction with RE.

Published
2002
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4. QTL dissection of Lag phase in wine fermentation reveals a new translocation responsible for Saccharomyces cerevisiae adaptation to sulfite

Author

Pascal Durrens, Adrien Zimmer, Cécile Durand, Nicolás Loira, Philippe Marullo, David James Sherman, Laffort [Floirac], Institut de Veille Sanitaire (INVS), Laboratoire Bordelais de Recherche en Informatique (LaBRI), Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB), Models and Algorithms for the Genome ( MAGNOME), Centre National de la Recherche Scientifique (CNRS)-Université de Bordeaux (UB)-Inria Bordeaux - Sud-Ouest, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria), Faculté d'Oenologie [Bordeaux II], Université Bordeaux Segalen - Bordeaux 2-Institut des Sciences de la Vigne et du Vin (ISVV), Université de Bordeaux (UB)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Centre National de la Recherche Scientifique (CNRS), Inria Bordeaux - Sud-Ouest, and Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Candidate gene, Saccharomyces cerevisiae Proteins, Heredity, quantitative genetics, Saccharomyces cerevisiae, Quantitative Trait Loci, lcsh:Medicine, Chromosomal translocation, Wine, Yeast and Fungal Models, Biology, Quantitative trait locus, Microbiology, polymorphisme génétique, Chromosomal Disorders, Model Organisms, vitis vinifera, Genetics, vin, saccharomyces cerevisiae, lcsh:Science, Gene, Fermentation in winemaking, Evolutionary Biology, Multidisciplinary, fermentation alcoolique, Quantitative Traits, qtl, lcsh:R, food and beverages, Human Genetics, Genomics, biology.organism_classification, Trait Locus, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Yeast, genome sequencing, Yeast in winemaking, oenologie, Fermentation, Translocations, oenology, lcsh:Q, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], Research Article, Biotechnology
Abstract

International audience; Quantitative genetics and QTL mapping are efficient strategies for deciphering the genetic polymorphisms that explain the phenotypic differences of individuals within the same species. Since a decade, this approach has been applied to eukaryotic microbes such as Saccharomyces cerevisiae in order to find natural genetic variations conferring adaptation of individuals to their environment. In this work, a QTL responsible for lag phase duration in the alcoholic fermentation of grape juice was dissected by reciprocal hemizygosity analysis. After invalidating the effect of some candidate genes, a chromosomal translocation affecting the lag phase was brought to light using de novo assembly of parental genomes. This newly described translocation (XV-t-XVI) involves the promoter region of ADH1 and the gene SSU1 and confers an increased expression of the sulfite pump during the first hours of alcoholic fermentation. This translocation constitutes another adaptation route of wine yeast to sulfites in addition to the translocation VIII-t-XVI previously described. A population survey of both translocation forms in a panel of domesticated yeast strains suggests that the translocation XV-t-XVI has been empirically selected by human activity.

Published
2014
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5. Genomic Exploration of the Hemiascomycetous Yeasts: 4. The genome ofSaccharomyces cerevisiaerevisited

Author

Bernard Dujon, Arnaud Perrin, Micheline Wésolowski-Louvel, Emmanuel Talla, Elisabeth Bon, Monique Bolotin-Fukuhara, Claire Toffano-Nioche, Jacky de Montigny, Serge Casaregola, Odile Ozier-Kalogeropoulos, Michel Aigle, Gaëlle Blandin, Jean-Luc Souciet, Serge Potier, Cécile Neuvéglise, Fredj Tekaia, Christian Marck, Bertrand Llorente, Claude Gaillardin, Andrée Lépingle, Alain Malpertuy, Pascal Durrens, Laboratoire Bordelais de Recherche en Informatique (LaBRI), Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB), Microbiologie et Génétique Moléculaire (MGM), Institut National de la Recherche Agronomique (INRA)-Institut National Agronomique Paris-Grignon (INA P-G)-Centre National de la Recherche Scientifique (CNRS), Génétique Moléculaire des Levures, Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Unité de Microbiologie et génétique (UMG), Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université de Lyon-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon, Institut de génétique et microbiologie [Orsay] (IGM), Université Paris-Sud - Paris 11 (UP11)-Centre National de la Recherche Scientifique (CNRS), Génétique moléculaire, génomique, microbiologie (GMGM), Université Louis Pasteur - Strasbourg I-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Université Sciences et Technologies - Bordeaux 1-Université Bordeaux Segalen - Bordeaux 2, Université de Bordeaux (UB)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Centre National de la Recherche Scientifique (CNRS), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National des Sciences Appliquées de Lyon (INSA Lyon), and Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Transposable element, Sequence analysis, Annotation, Genes, Fungal, [INFO.INFO-OH]Computer Science [cs]/Other [cs.OH], Intron, Saccharomyces cerevisiae, Biophysics, [SDV.BC]Life Sciences [q-bio]/Cellular Biology, Biochemistry, Genome, Open Reading Frames, Pseudogene, 03 medical and health sciences, Ascomycota, RNA, Transfer, Structural Biology, Genetics, Family, Frameshift, Molecular Biology, Gene, 030304 developmental biology, Sequence (medicine), 0303 health sciences, biology, 030302 biochemistry & molecular biology, Cell Biology, biology.organism_classification, Multigene Family, Transfer RNA, DNA, Intergenic, Chromosomes, Fungal, Genome, Fungal, Sequence Alignment
Abstract

International audience; Since its completion more than 4 years ago, the sequence of Saccharomyces cerevisiae has been extensively used and studied. The original sequence has received a few corrections, and the identification of genes has been completed, thanks in particular to transcriptome analyses and to specialized studies on introns, tRNA genes, transposons or multigene families. In order to undertake the extensive comparative sequence analysis of this program, we have entirely revisited the S. cerevisiae sequence using the same criteria for all 16 chromosomes and taking into account publicly available annotations for genes and elements that cannot be predicted. Comparison with the other yeast species of this program indicates the existence of 50 novel genes in segments previously considered as ‘intergenic’ and suggests extensions for 26 of the previously annotated genes.

Published
2000
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6. Genomic Exploration of the Hemiascomycetous Yeasts: 18. Comparative analysis of chromosome maps and synteny withSaccharomyces cerevisiae

Author

Michel Aigle, Gaëlle Blandin, Patrick Wincker, Micheline Wésolowski-Louvel, Elisabeth Bon, Monique Bolotin-Fukuhara, Fredj Tekaia, Jean-Luc Souciet, Odile Ozier-Kalogeropoulos, Cécile Neuvéglise, Claude Gaillardin, Serge Potier, Philippe Brottier, Jean Weissenbach, William Saurin, François Artiguenave, Bernard Dujon, Claire Toffano-Nioche, Jacky de Montigny, Serge Casaregola, Alain Malpertuy, Pascal Durrens, Bertrand Llorente, and Andrée Lépingle

Subjects
Duplication, Saccharomyces cerevisiae, Biophysics, Translocation, Biology, Biochemistry, Genome, Deletion, Redundancy, Ascomycota, Structural Biology, Molecular evolution, Gene Duplication, Gene Order, Gene duplication, Genetics, Molecular Biology, Gene, Synteny, Chromosomal inversion, Inversion, Chromosome Mapping, Computational Biology, Chromosome, Genomics, Cell Biology, biology.organism_classification, Loss, Chromosomes, Fungal, Gene Deletion
Abstract

We have analyzed the evolution of chromosome maps of Hemiascomycetes by comparing gene order and orientation of the 13 yeast species partially sequenced in this program with the genome map of Saccharomyces cerevisiae. From the analysis of nearly 8000 situations in which two distinct genes having homologs in S. cerevisiae could be identified on the sequenced inserts of another yeast species, we have quantified the loss of synteny, the frequency of single gene deletion and the occurrence of gene inversion. Traces of ancestral duplications in the genome of S. cerevisiae could be identified from the comparison with the other species that do not entirely coincide with those identified from the comparison of S. cerevisiae with itself. From such duplications and from the correlation observed between gene inversion and loss of synteny, a model is proposed for the molecular evolution of Hemiascomycetes. This model, which can possibly be extended to other eukaryotes, is based on the reiteration of events of duplication of chromosome segments, creating transient merodiploids that are subsequently resolved by single gene deletion events.

Published
2000
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7. A network of proteins around Rvs167p and Rvs161p, two proteins related to the yeast actin cytoskeleton

Author

Pascal Durrens, Elisabeth Bon, Masayuki Iwase, Akio Toh-e, Patricia Recordon-Navarro, and Michel Aigle

Subjects
Saccharomyces cerevisiae Proteins, Genetic Vectors, Saccharomyces cerevisiae, Bioengineering, Endocytosis, Applied Microbiology and Biotechnology, Biochemistry, Fungal Proteins, Open Reading Frames, Two-Hybrid System Techniques, Genetics, ORFS, Chromosomes, Artificial, Yeast, Cytoskeleton, Actin, Binding Sites, biology, Microfilament Proteins, Actin cytoskeleton, biology.organism_classification, Actins, Yeast, Cell biology, Cytoskeletal Proteins, Protein Binding, Biotechnology
Abstract

The Rvs161p and Rvs167p proteins of Saccharomyces cerevisiae, homologues of higher eukaryotes' amphiphysins, associate with actin and appear to be involved in several functions related to the actin cytoskeleton. In order to identify partners of the Rvsp proteins, yeast libraries constructed in two-hybrid vectors were screened using either Rvs167p or Rvs161p as a bait. The selected candidates, representing 34 ORFs, were then tested against both Rvsp proteins, as well as domains of Rvs167p or Rvs161p. Among the most significant ones, 24 ORFs were specific preys of Rvs167p only and two gave interactions with Rvs161p only. Interestingly, five ORFs were preys of both Rvs161p and Rvs167p (RVS167, LAS17, YNL094w, YMR192w and YPL249c). Analysis of putative functions of the candidates confirm involvement of the Rvsp in endocytosis/vesicle traffic, but also opens possible new fields, such as nuclear functions. Copyright © 2000 John Wiley & Sons, Ltd.

Published
2000
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8. Protein–protein interaction between the RVS161 and RVS167 gene products of Saccharomyces cerevisiae

Author

Michel Aigle, Patricia Navarro, and Pascal Durrens

Subjects
Saccharomyces cerevisiae Proteins, Protein Conformation, Blotting, Western, Saccharomyces cerevisiae, Biophysics, Biochemistry, Protein Structure, Secondary, Protein–protein interaction, Fungal Proteins, Protein structure, Genes, Reporter, Structural Biology, Cytoskeleton, Molecular Biology, Gene, biology, Chemistry, Microfilament Proteins, Microfilament Protein, beta-Galactosidase, biology.organism_classification, Precipitin Tests, Blot, Cytoskeletal Proteins, Dimerization, Function (biology), Plasmids
Abstract

As previous studies indicated that the RVS161 and RVS167 gene products of Saccharomyces cerevisiae seem to be involved in the same cellular function, we considered the possibility of a complex between the proteins encoded by these two genes. Using the two hybrid system, we have shown that Rvs167p interacts with Rvs161p, through its N-terminal domain which contains predicted coiled-coil structures. Moreover, if a tagged Rvs 167p protein was immuno adsorbed under non-denaturing conditions, it brought along the Rvs161p protein. These results confirmed the hypothesis of an in vivo complex between the two proteins.

Published
1997
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9. Evidence for a branched pathway in the polarized cell division of Saccharomyces cerevisiae

Author

Pascal Durrens, E. Revardel, M. Bonneu, and Michel Aigle

Subjects
Genetics, Mutation, Mating type, Models, Genetic, Cell division, biology, Genes, Fungal, Mutant, Saccharomyces cerevisiae, Cell Polarity, Epistasis, Genetic, General Medicine, Genes, Mating Type, Fungal, medicine.disease_cause, biology.organism_classification, Phenotype, Fungal Proteins, medicine, Epistasis, Gene, Cell Division
Abstract

Cells of Saccharomyces cerevisiae can choose a bud site in one of two different spatial patterns (axial or bipolar) determined by their mating type. Genes important for bud-site selection have been identified and a linear model describing the hierarchy of these genes was proposed. We have uncovered a new class of genes which is required only for the bipolar pattern. The phenotype of the corresponding mutants coupled with epistasis experiments with some budding mutants already described suggest the existence of specific genes for the bipolar pathway.

Published
1995
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10. Single QTL mapping and nucleotide-level resolution of a physiologic trait in wine Saccharomyces cerevisiae strains

Author

Gaël Yvert, Isabelle Masneuf-Pomarède, Pascal Durrens, Denis Dubourdieu, Michel Aigle, Philippe Marullo, Marina Bely, Faculté d'Oenologie [Bordeaux II], Université Bordeaux Segalen - Bordeaux 2-Institut des Sciences de la Vigne et du Vin (ISVV), Laboratoire de Biologie Moléculaire de la Cellule (LBMC), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon, Models and Algorithms for the Genome (MAGNOME), INRIA Futurs, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Université Sciences et Technologies - Bordeaux 1-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de biologie moléculaire de la cellule ( BMC ), École normale supérieure - Lyon ( ENS Lyon ) -Institut National de la Recherche Agronomique ( INRA ) -Université Claude Bernard Lyon 1 ( UCBL ), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique ( CNRS ), Models and Algorithms for the Genome ( MAGNOME ), Institut National de Recherche en Informatique et en Automatique ( Inria ) -Institut National de Recherche en Informatique et en Automatique ( Inria ) -Université Sciences et Technologies - Bordeaux 1-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Centre National de la Recherche Scientifique ( CNRS ), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), and Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Université Sciences et Technologies - Bordeaux 1 (UB)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Nonsynonymous substitution, QTL mapping, Saccharomyces cerevisiae Proteins, Nitrogen, Saccharomyces cerevisiae, Quantitative Trait Loci, Wine, Quantitative trait locus, Applied Microbiology and Biotechnology, Microbiology, Genome, Polymorphism, Single Nucleotide, 03 medical and health sciences, Genotype, Asparaginase, Pyrophosphatases, 030304 developmental biology, Acetic Acid, 2. Zero hunger, Genetics, 0303 health sciences, [SDV.GEN]Life Sciences [q-bio]/Genetics, biology, 030306 microbiology, DNA microarray, Chromosome Mapping, Reproducibility of Results, General Medicine, Quantitative genetics, Carbon Dioxide, biology.organism_classification, ASP1, Aneuploidy, Yeast, wine fermentation, Phenotype, Chromosomes, Fungal, Genome, Fungal, [ SDV.GEN ] Life Sciences [q-bio]/Genetics
Abstract

International audience; Natural Saccharomyces cerevisiae yeast strains exhibit very large genotypic and phenotypic diversity. However, the link between phenotype variation and genetic determinism is still difficult to identify, especially in wild populations. Using genome hybridization on DNA microarrays, it is now possible to identify single-feature polymorphisms among divergent yeast strains. This tool offers the possibility of applying quantitative genetics to wild yeast strains. In this instance, we studied the genetic basis for variations in acetic acid production using progeny derived from two strains from grape must isolates. The trait was quantified during alcoholic fermentation of the two strains and 108 segregants derived from their crossing. A genetic map of 2212 markers was generated using oligonucleotide microarrays, and a major quantitative trait locus (QTL) was mapped with high significance. Further investigations showed that this QTL was due to a nonsynonymous single-nucleotide polymorphism that targeted the catalytic core of asparaginase type I (ASP1) and abolished its activity. This QTL was only effective when asparagine was used as a major nitrogen source. Our results link nitrogen assimilation and CO(2) production rate to acetic acid production, as well as, on a broader scale, illustrating the specific problem of quantitative genetics when working with nonlaboratory microorganisms.

Published
2007
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11. A novel link between a Rab GTPase and Rvs proteins: the yeast amphiphysin homologues

Author

Michel Aigle, Nicolas Talarek, Axelle Balguerie, Pascal Durrens, Institut de biochimie et génétique cellulaires (IBGC), Université Bordeaux Segalen - Bordeaux 2-Centre National de la Recherche Scientifique (CNRS), Laboratoire Bordelais de Recherche en Informatique (LaBRI), Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB), Unité de Microbiologie et génétique (UMG), Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université Claude Bernard Lyon 1 (UCBL), and Université de Lyon

Subjects
Saccharomyces cerevisiae Proteins, Molecular Sequence Data, Clinical Biochemistry, Mutant, Saccharomyces cerevisiae, Fus2p, [INFO.INFO-OH]Computer Science [cs]/Other [cs.OH], GTPase, [SDV.BC.BC]Life Sciences [q-bio]/Cellular Biology/Subcellular Processes [q-bio.SC], Biology, Biochemistry, SH3 domain, src Homology Domains, 03 medical and health sciences, 0302 clinical medicine, Two-Hybrid System Techniques, GAP protein (Gyp5p, Ymr192p), [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Amino Acid Sequence, Vesicular traffic, Cytokinesis, 030304 developmental biology, Genetics, 0303 health sciences, Sequence Homology, Amino Acid, Microfilament Proteins, Cell Biology, General Medicine, biology.organism_classification, Fusion protein, Cell biology, Rvsp, rab GTP-Binding Proteins, Amphiphysin, Rab, 030217 neurology & neurosurgery
Abstract

The BAR proteins are a well-conserved family of proteins including Rvsp in yeast, amphiphysins and Bin proteins in mammals. In yeast, as in mammals, BAR proteins are known to be implicated in vesicular traffic. The Gyp5p (Ypl249p) and Ymr192p proteins interact in two-hybrid tests with both Rvs161p and Rvs167p. Gyp5p is a Ypt/Rab-specific GAP and Ymr192p is highly similar to Gyp5p. To specify the interaction between Rvsp and Gyp5p, we used two-hybrid tests to determine the domains necessary for these interactions. The specific SH3 domain of Rvs167p interacted with the N-terminal domain of Gyp5p. Moreover, Gyp5p could form a homodimer. Fus2 protein is a specific partner of Rvs161p in two-hybrid tests. To characterize the functional relationships between these five proteins, we have studied cellular phenotypes in single, double and triple mutant strains for which rvs mutants present defects, such as polarity, cell fusion and meiosis. Phenotypic analysis showed that Gyp5p, Ymr192p and Fus2p were involved in bipolar budding pattern and in meiosis. Specific epistasis or suppressive phenomena were found between the five mutations. Finally, The Gyp5p–GFP fusion protein was localized at the bud tip during apical growth and at the mother-bud neck during cytokinesis. Moreover, Rvs167p and Rvs161p were shown to be essential for the correct localization of Gyp5p. Altogether, these data support the hypothesis that both Rvsp proteins act in vesicular traffic through physical and functional interactions with Ypt/Rab regulators. Copyright © 2004 John Wiley & Sons, Ltd.

Published
2005
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12. Genome evolution in yeasts

Author

Valérie Barbe, Laurence Cattolico, Isabelle Lesur, Alix Kerrest, Hélène Ferry-Dumazet, Fabrice Confanioleri, Serge Casaregola, Emmanuel Talla, Véronique Anthouard, Jean-Marie Beckerich, Laurence Ma, Odile Ozier-Kalogeropoulos, Nicolas Jauniaux, Nicolas Goffard, Jacky de Montigny, David James Sherman, Antoine de Daruvar, Serge Potier, Guy-Franck Richard, Romain Koszul, Pascal Durrens, Anna Babour, Sophie Oztas, Emmanuelle Beyne, Christian Marck, Patrick Wincker, Emmanuelle Fabre, Stefan Pellenz, Bernard Dujon, Florence Hantraye, Eric Westhof, Cécile Fairhead, Micheline Wésolowski-Louvel, Cécile Neuvéglise, Gilles Fischer, Laurence Despons, Christophe Hennequin, Jean Weissenbach, Marie-Laure Straub, Audrey Suleau, Stéphanie Barnay, Jean-Marc Nicaud, Macha Nikolski, Claude Gaillardin, Claudine Bleykasten, Jean-Luc Souciet, Fredj Tekaia, Philippe Joyet, Rym Kachouri, Sylvie Blanchin, Bénédicte Wirth, Héloïse Muller, Christiane Bouchier, Maria Zeniou-Meyer, Ingrid Lafontaine, Jeanne Boyer, Monique Bolotin-Fukuhara, Ivan Zivanovic, Claude Scarpelli, Bernard Caudron, Agnès Thierry, Dominique Swennen, Alexis Groppi, Anita Boisramé, Michel Aigle, Lionel Frangeul, Marc Lemaire, Génétique Moléculaire des Levures, Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Laboratoire Bordelais de Recherche en Informatique (LaBRI), Université de Bordeaux (UB)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Centre National de la Recherche Scientifique (CNRS), Centre de Bioinformatique de Bordeaux (CBIB), CGFB, Institut de biochimie et génétique cellulaires (IBGC), Université Bordeaux Segalen - Bordeaux 2-Centre National de la Recherche Scientifique (CNRS), Collection de Levures d'Intérêt Biotechnologique et Laboratoire de Génétique Moléculaire et Cellulaire, Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Dynamique, évolution et expression de génomes de microorganismes (DEEGM), Université Louis Pasteur - Strasbourg I-Centre National de la Recherche Scientifique (CNRS), Service de Biochimie, Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Génomique (Plate-Forme) - Genomics Platform, Institut Pasteur [Paris] (IP), Génomique métabolique (UMR 8030), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Institut de génétique et microbiologie [Orsay] (IGM), Université Paris-Sud - Paris 11 (UP11)-Centre National de la Recherche Scientifique (CNRS), Génétique des Interactions Macromoléculaires, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Unité de Microbiologie et génétique (UMG), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS), Architecture et réactivité de l'ARN (ARN), Logiciels et Banques de Données, Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Université Sciences et Technologies - Bordeaux 1-Université Bordeaux Segalen - Bordeaux 2, Génomique (Plate-Forme), Institut Pasteur [Paris], Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université de Lyon-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon, and Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université Claude Bernard Lyon 1 (UCBL)

Subjects
MESH: Tandem Re, MESH: Research Support, Non-U.S. Gov't, Genome, MESH: Saccharomyces cerevisiae Proteins, RNA, Transfer, Gene Duplication, Yeasts, Conserved Sequence, MESH: Evolution, Molecular, Segmental duplication, Genomic organization, Genetics, SACCHAROMYCES CEREVISIAE, 0303 health sciences, Multidisciplinary, MESH: Conserved Sequence, MESH: Yeasts, MESH: Gene Duplication, MESH: Synteny, Genome project, MESH: Chromosomes, Fungal, Tandem Repeat Sequences, MESH: Genome, Fungal, Chromosomes, Fungal, Genome, Fungal, GENETIC MAPPING, Genome evolution, Saccharomyces cerevisiae Proteins, Genes, Fungal, Molecular Sequence Data, Biology, Synteny, Evolution, Molecular, 03 medical and health sciences, GENOME ORGANIZATION, Molecular evolution, YEAST, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Gene, 030304 developmental biology, Comparative genomics, STRUCTURE DU GENOME, MESH: Molecular Sequence Data, 030306 microbiology, MESH: RNA, Transfer, MOLECULAR EVOLUTION, MESH: Tandem Repeat Sequences, Evolutionary biology, RNA, Ribosomal, MESH: RNA, Ribosomal, MESH: Genes, Fungal
Abstract

Identifying the mechanisms of eukaryotic genome evolution by comparative genomics is often complicated by the multiplicity of events that have taken place throughout the history of individual lineages, leaving only distorted and superimposed traces in the genome of each living organism. The hemiascomycete yeasts, with their compact genomes, similar lifestyle and distinct sexual and physiological properties, provide a unique opportunity to explore such mechanisms. We present here the complete, assembled genome sequences of four yeast species, selected to represent a broad evolutionary range within a single eukaryotic phylum, that after analysis proved to be molecularly as diverse as the entire phylum of chordates. A total of approximately 24,200 novel genes were identified, the translation products of which were classified together with Saccharomyces cerevisiae proteins into about 4,700 families, forming the basis for interspecific comparisons. Analysis of chromosome maps and genome redundancies reveal that the different yeast lineages have evolved through a marked interplay between several distinct molecular mechanisms, including tandem gene repeat formation, segmental duplication, a massive genome duplication and extensive gene loss.

Published
2004
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13. HIV-1 integrase interacts with yeast microtubule-associated proteins

Author

Michel Fournier, Elisabeth Bon, Vincent Parissi, Christina Calmels, Vaea Richard de Soultrait, Pascal Durrens, Laura Tarrago-Litvak, Anne Caumont, Cécile Desjobert, and Patricia Recordon

Subjects
Microtubule-associated protein, Biophysics, HIV Integrase, Saccharomyces cerevisiae, Biology, Biochemistry, Spindle pole body, law.invention, Structural Biology, Microtubule, law, Genetics, Humans, Genomic library, Binding Sites, Molecular biology, Yeast, Recombinant Proteins, Cell biology, Integrase, genomic DNA, Recombinant DNA, biology.protein, HIV-1, Microtubule-Associated Proteins, Protein Binding
Abstract

The human immunodeficiency virus type 1 (HIV-1) integrase (IN) mediates the insertion of viral DNA into the human genome. In addition to IN, cellular and viral proteins are associated to proviral DNA in the so-called preintegration complex (PIC). We previously reported that the expression of HIV-1 IN in yeast leads to the emergence of a lethal phenotype. This effect may be linked to the IN activity on infected human cells where integration requires the cleavage of genomic DNA. To isolate and characterize potential cellular partners of HIV-1 IN, we used it as a bait in a two-hybrid system with a yeast genomic library. IN interacted with proteins belonging to the microtubule network, or involved in the protein synthesis apparatus. We focused our interest on one of the selected inserts, L2, which corresponds to the C-end half of the yeast STU2p, a microtubule-associated protein (MAP). STU2p is an essential component of the yeast spindle pole body (SPB), which is able to bind microtubules in vitro. After expressing and purifying L2 as a recombinant protein, we showed its binding to IN by ELISA immunodetection. L2 was also able to inhibit IN activity in vitro. In addition, the effect of L2 was tested using the “lethal yeast phenotype”. The coexpression of IN and the L2 peptide abolished the lethal phenotype, thus showing important in vivo interactions between IN and L2. The identification of components of the microtubule network associated with IN suggest a role of this complex in the transport of HIV-1 IN present in the PIC to the nucleus, as already described for other human viruses.

Published
2002

14. The complete genome of Blastobotrys (Arxula) adeninivorans LS3 - a yeast of biotechnological interest

Author

Rüdiger Bode, Martin Mascher, Serge Casaregola, Anasua Sarkar, Guilhem Savel, Patrick Wincker, Valérie Barbe, Martin Giersberg, Marina Marcet-Houben, Keith Baronian, Nils Stein, Véronique Leh-Louis, Christine Sacerdot, Guy-Franck Richard, Jan Riechen, Ingrid Lafontaine, Jean Luc Souciet, Urs Hähnel, Eric Westhof, Joseph Schacherer, Uwe Scholz, Sebastian Worch, Sebastian Beier, Pascal Durrens, Erik Böer, Anke Trautwein-Schult, Christian Marck, Toni Gabaldón, Cécile Fairhead, Anja Hartmann, Claire Jubin, Bernard Dujon, Cécile Neuvéglise, Małgorzata Czernicka, Claudine Bleykasten, David James Sherman, Laurence Despons, Marie Laure Straub, Paul P. Jung, Marc Lemaire, Dagmara Jankowska, Tiphaine Martin, Benoit Vacherie, Emmanuel Talla, Agnès Thierry, José Almeida Cruz, André Goffeau, Gotthard Kunze, Claude Gaillardin, Philippe Baret, Guillaume Morel, Przemysław Piotr Gierski, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, Yeast Genetics, Leibniz Institute of Plant Research (IPK), MICrobiologie de l'ALImentation au Service de la Santé (MICALIS), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Institute of Plant Biology and Biotechnology, University of Agriculture in Krakow, Laboratoire Bordelais de Recherche en Informatique (LaBRI), Centre National de la Recherche Scientifique (CNRS)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Université Sciences et Technologies - Bordeaux 1-Université Bordeaux Segalen - Bordeaux 2, Models and Algorithms for the Genome ( MAGNOME), Inria Bordeaux - Sud-Ouest, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS), Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Universitat Pompeu Fabra [Barcelona], Architecture et Réactivité de l'ARN (ARN), Institut de biologie moléculaire et cellulaire (IBMC), Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de chimie bactérienne (LCB), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Institut de Biologie et de Technologies de Saclay (IBITECS), Université Paris-Saclay-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Université catholique de Louvain, Institut des Sciences de la Vie, Institut de Génomique d'Evry (IG), Institut de Biologie François JACOB (JACOB), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay, Earth and Life Institute [Louvain-La-Neuve] (ELI), Université Catholique de Louvain (UCL), School of Biological Sciences, University of Canterbury, Institute of Biochemistry, Universität Greifswald - University of Greifswald, Université de Strasbourg (UNISTRA), Institut de génétique et microbiologie [Orsay] (IGM), Université Paris-Sud - Paris 11 (UP11)-Centre National de la Recherche Scientifique (CNRS), Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, Génomique métabolique (UMR 8030), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), Génétique moléculaire, génomique, microbiologie (GMGM), Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA), Génétique Moléculaire des Levures, Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Génétique moléculaire des levures (YMG), Microbiologie, adaptation et pathogénie (MAP), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS), This work was supported in part by funding from the Consortium National de Recherche en Génomique (CNRG) to Génoscope, from CNRS (GDR 2354, Génolevures), ANR (ANR-05-BLAN-0331, GENARISE). The computing framework was supported by the funding of the University of Bordeaux 1, the Aquitaine Région in the program ' Génotypage et Génomique Comparée ' , the ACI IMPBIO ' Génolevures En Ligne ' and INRIA. We thank the System and Network Administration team in LaBRI for excellent help and advice. J.A.C. is supported by the PhD Program in Computational Biology of the Instituto Gulbenkian de Ciência, Portugal (sponsored by Fundação Calouste Gulbenkian, Siemens SA, and Fundação para a Ciência e Tecnologia, SFRH/BD/33528/2008). M.C. research was supported by a grant of the Deutscher Akademischer Austauschdienst (DAAD). T.G. research was partly supported by a grant from the Spanish Ministry of Economy and Competitiveness (BIO2012-37161)., Leibniz Institute of Plant Genetics and Crop Plant Research [Gatersleben] (IPK-Gatersleben), Université de Bordeaux (UB)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Centre National de la Recherche Scientifique (CNRS), Universitat Pompeu Fabra [Barcelona] (UPF), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay, Université Catholique de Louvain = Catholic University of Louvain (UCL), Université Paris-Saclay-Institut de Biologie François JACOB (JACOB), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), University of Canterbury [Christchurch], International Institute of Molecular and Cell Biology [Warsaw] (IIMCB), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS), Kunze, Gotthard, Neuvéglise, Cécile, UCL - SST/ELI/ELIA - Agronomy, Centre National de la Recherche Scientifique (CNRS)-Université de Bordeaux (UB)-Inria Bordeaux - Sud-Ouest, and Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)

Subjects
Yarrowia lipolytica, n-butanol, yeast, genome, tannic acid, metabolism, biotechnology, [SDV.BIO]Life Sciences [q-bio]/Biotechnology, Technological development, Butyric acid, Applied Microbiology and Biotechnology, Genome, Blastobotrys, Saccharomycotina, [INFO.INFO-BT]Computer Science [cs]/Biotechnology, N-butanol, 2. Zero hunger, 0303 health sciences, biology, Segmental duplications, Genomics, Phylogenetics, General Energy, Biochemistry, Biotechnology, Nitrogen, Saccharomyces cerevisiae, Biotecnologia agrícola, Computational biology, Management, Monitoring, Policy and Law, Biotechnological potentials, Arxula, Arxula adeninivorans, 03 medical and health sciences, Carbon and nitrogen, 030304 developmental biology, Saccharomycetes, Comparative genomics, Tannic acid, 030306 microbiology, Renewable Energy, Sustainability and the Environment, Protein, Research, Fundamental studies, Yarrowia, Llevats -- Genètica, biology.organism_classification, Yeast, Carbon, Metabolism, Genes, Organic acid
Abstract

Background: The industrially important yeast Blastobotrys (Arxula) adeninivorans is an asexual hemiascomycete phylogenetically very distant from Saccharomyces cerevisiae. Its unusual metabolic flexibility allows it to use a wide range of carbon and nitrogen sources, while being thermotolerant, xerotolerant and osmotolerant./nResults: The sequencing of strain LS3 revealed that the nuclear genome of A. adeninivorans is 11.8 Mb long and consists of four chromosomes with regional centromeres. Its closest sequenced relative is Yarrowia lipolytica, although mean conservation of orthologs is low. With 914 introns within 6116 genes, A. adeninivorans is one of the most intron-rich hemiascomycetes sequenced to date. Several large species-specific families appear to result from multiple rounds of segmental duplications of tandem gene arrays, a novel mechanism not yet described in yeasts. An analysis of the genome and its transcriptome revealed enzymes with biotechnological potential, such as two extracellular tannases (Atan1p and Atan2p) of the tannic-acid catabolic route, and a new pathway for the assimilation of n-butanol via butyric aldehyde and butyric acid. Conclusions: The high-quality genome of this species that diverged early in Saccharomycotina will allow further fundamental studies on comparative genomics, evolution and phylogenetics. Protein components of different pathways for carbon and nitrogen source utilization were identified, which so far has remained unexplored in yeast, offering clues for further biotechnological developments. In the course of identifying alternative microorganisms for biotechnological interest, A. adeninivorans has already proved its strengthened competitiveness as a promising cell factory for many more applications. This work was supported in part by funding from the Consortium National de Recherche en Génomique (CNRG) to Génoscope, from CNRS (GDR 2354, Génolevures), ANR (ANR-05-BLAN-0331, GENARISE). The computing framework was supported by the funding of the University of Bordeaux 1, the Aquitaine Région in the program “Génotypage et Génomique Comparée”, the ACI IMPBIO “Génolevures En Ligne” and INRIA. We thank the System and Network Administration team in LaBRI for excellent help and advice. J.A.C. is supported by the PhD Program in Computational Biology of the Instituto Gulbenkian de Ciência, Portugal (sponsored by Fundação Calouste Gulbenkian, Siemens SA, and Fundação para a Ciência e Tecnologia; SFRH/BD/33528/2008). M.C. research was supported by a grant of the Deutscher Akademischer Austauschdienst (DAAD). T.G. research was partly supported by a grant from the Spanish Ministry of Economy and Competitiveness (BIO2012-37161). B.D. is a member of Institut Universitaire de France

Published
2014
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15. Genomic exploration of the hemiascomycetous yeasts: 5. Saccharomyces bayanus var. uvarum

Author

Cécile Neuvéglise, François Artiguenave, Pascal Durrens, Elisabeth Bon, Serge Casaregola, Patrick Wincker, Michel Aigle, Microbiologie et Génétique Moléculaire (MGM), and Institut National de la Recherche Agronomique (INRA)-Institut National Agronomique Paris-Grignon (INA P-G)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Genome evolution, Retroelements, Saccharomyces cerevisiae, Centromere, Molecular Sequence Data, Biophysics, Saccharomyces bayanus, Introgression, Translocation, Retrotransposon, [SDV.BC]Life Sciences [q-bio]/Cellular Biology, Biology, Biochemistry, 03 medical and health sciences, Contig Mapping, Saccharomyces, Ascomycota, Structural Biology, Gene Order, Genetics, ORFS, Molecular Biology, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, Synteny, 0303 health sciences, 030306 microbiology, Cell Biology, Sequence Analysis, DNA, Ty, biology.organism_classification, Open reading frame, Chromosomes, Fungal, Genome, Fungal
Abstract

Saccharomyces bayanus var. uvarum investigated here is the species closest to Saccharomyces cerevisiae. Random sequence tags (RSTs) allowed us to identify homologues to 2789 open reading frames (ORFs) in S. cerevisiae, ORFs duplicated in S. uvarum but not in S. cerevisiae, centromeres, tRNAs, homologues of Ty1/2 and Ty4 retrotransposons, and a complete rDNA repeat. Only 13 RSTs seem to be homologous to sequences in other organisms but not in S. cerevisiae. As the synteny between the two species is very high, cases in which synteny is lost suggest special mechanisms of genome evolution. The corresponding RSTs revealed that S. uvarum can exist without any S. cerevisiae DNA introgression. Accession numbers are from AL397139 to AL402278 in the EMBL databank.

Published
2001

16. Evolution of gene order in the genomes of two related yeast species

Author

Bernard Dujon, Claude Gaillardin, Cécile Neuvéglise, Gilles Fischer, Pascal Durrens, Laboratoire Bordelais de Recherche en Informatique (LaBRI), Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB), and Centre National de la Recherche Scientifique (CNRS)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Université Sciences et Technologies - Bordeaux 1-Université Bordeaux Segalen - Bordeaux 2

Subjects
0106 biological sciences, Genetic Linkage, Genes, Fungal, Molecular Sequence Data, [INFO.INFO-OH]Computer Science [cs]/Other [cs.OH], Saccharomyces bayanus, Saccharomyces cerevisiae, 01 natural sciences, Genome, Translocation, Genetic, Evolution, Molecular, Saccharomyces, 03 medical and health sciences, Gene Duplication, Gene Order, Gene duplication, Gene cluster, Genetics, Gene, Genetics (clinical), 030304 developmental biology, Synteny, Chromosomal inversion, Recombination, Genetic, 0303 health sciences, Concerted evolution, biology, biology.organism_classification, Chromosome Inversion, Chromosomes, Fungal, Genome, Fungal, Gene Deletion, 010606 plant biology & botany
Abstract

Changes in gene order between the genomes of two related yeast species, Saccharomyces cerevisiae and Saccharomyces bayanus var. uvarum were studied. From the dataset of a previous low coverage sequencing of the S. bayanus var.uvarum genome, 35 different synteny breakpoints between neighboring genes and two cases of local gene inversion were characterized in detail. The number and the type of the chromosomal rearrangements that have lead to these differences were identified. We show that evolution of gene order in the genomes of these two yeast species is driven mainly by gene duplication onto different chromosomes followed by differential loss of the repeated copies. In addition, local gene inversions also would result from a mechanism of gene duplication, but in an inverted orientation, followed by loss of the original copy. The identification of traces of anciently duplicated genes, called relics, show that the loss of duplicates is more frequently caused by the accumulation of numerous mutations in one of the two copies than by DNA deletion. Surprisingly, gross chromosomal rearrangements such as translocations have only a minor effect on gene order reshuffling as they account for [The sequence data have been submitted to the EMBL Library under accession nos. AJ316068 and AJ316069.]

Published
2001
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17. Genomic exploration of the hemiascomycetous yeasts: 21. Comparative functional classification of genes

Author

Elisabeth Bon, Jean Weissenbach, William Saurin, Patrick Wincker, Micheline Wésolowski-Louvel, Michel Termier, Claire Toffano-Nioche, Michel Aigle, Jacky de Montigny, Philippe Brottier, Bertrand Llorente, Andrée Lépingle, Claude Gaillardin, Alain Malpertuy, Pascal Durrens, Serge Casaregola, Jean-Luc Souciet, Monique Bolotin-Fukuhara, Serge Potier, Guillemette Duchateau-Nguyen, François Artiguenave, Odile Ozier-Kalogeropoulos, Fredj Tekaia, Bernard Dujon, Gaëlle Blandin, Cécile Neuvéglise, Laboratoire de Génétique Moléculaire et Cellulaire (INRA UMR216-URA1925), Institut National de la Recherche Agronomique (INRA), Institut de génétique et microbiologie [Orsay] (IGM), Université Paris-Sud - Paris 11 (UP11)-Centre National de la Recherche Scientifique (CNRS), Génétique Moléculaire des Levures, Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Institut de biochimie et génétique cellulaires (IBGC), Université Bordeaux Segalen - Bordeaux 2-Centre National de la Recherche Scientifique (CNRS), Structure et évolution des génomes (SEG), CNS-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Génétique moléculaire, génomique, microbiologie (GMGM), Université Louis Pasteur - Strasbourg I-Centre National de la Recherche Scientifique (CNRS), Unité de Microbiologie et génétique (UMG), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de génétique moléculaire et cellulaire, Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon, and Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Speciation, Biodiversity, MESH: Research Support, Non-U.S. Gov't, Biochemistry, MESH: Gene Amplification, MESH: Variation (Genetics), MESH: Yeast, Structural Biology, Yeasts, Gene cluster, MESH: Phylogeny, Phylogeny, Genetics, 0303 health sciences, biology, MESH: Genomics, MESH: Comparative Study, Genomics, MESH: Saccharomyces cerevisiae, Horizontal gene transfer, MESH: Fungal Proteins, Genes, Fungal, Saccharomyces cerevisiae, Biophysics, MESH: Ascomycota, MESH: Sequence Homology, Nucleic Acid, Fungal Proteins, 03 medical and health sciences, MESH: Software, Ascomycota, Species Specificity, Phylogenetics, Sequence Homology, Nucleic Acid, Gene family, MESH: Species Specificity, Molecular Biology, Gene, 030304 developmental biology, [SDV.GEN]Life Sciences [q-bio]/Genetics, 030306 microbiology, Gene Amplification, Genetic Variation, Cell Biology, 15. Life on land, biology.organism_classification, Yeast, MESH: Genes, Fungal, Software, Pathway
Abstract

We explored the biological diversity of hemiascomycetous yeasts using a set of 22 000 newly identified genes in 13 species through BLASTX searches. Genes without clear homologue in Saccharomyces cerevisiae appeared to be conserved in several species, suggesting that they were recently lost by S. cerevisiae. They often identified well-known species-specific traits. Cases of gene acquisition through horizontal transfer appeared to occur very rarely if at all. All identified genes were ascribed to functional classes. Functional classes were differently represented among species. Species classification by functional clustering roughly paralleled rDNA phylogeny. Unequal distribution of rapidly evolving, ascomycete-specific, genes among species and functions was shown to contribute strongly to this clustering. A few cases of gene family amplification were documented, but no general correlation could be observed between functional differentiation of yeast species and variations of gene family sizes. Yeast biological diversity seems thus to result from limited species-specific gene losses or duplications, and for a large part from rapid evolution of genes and regulatory factors dedicated to specific functions.

Published
2000
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18. Characterization of a new gene family developing pleiotropic phenotypes upon mutation in Saccharomyces cerevisiae

Author

Emmanuelle Revardel, Michel Aigle, Marc Bonneau, and Pascal Durrens

Subjects
Saccharomyces cerevisiae Proteins, Mutant, Genes, Fungal, Molecular Sequence Data, Biophysics, Pair-rule gene, Saccharomyces cerevisiae, Gene mutation, Biology, Biochemistry, Gene dosage, Fungal Proteins, Structural Biology, Gene cluster, Genetics, Gene family, Amino Acid Sequence, Gene, Base Sequence, Microfilament Proteins, Cortical actin cytoskeleton, Cytoskeletal Proteins, Phenotype, Mutation, Sequence Alignment
Abstract

The aim of this paper is to gather and complete data about four members of a new gene family. Mutation in SUR4 gene was originally selected as a suppressor of defects caused by mutations in RVS161 or RVS167 genes. Cloning and sequencing of the SUR4 gene were performed. The deduced protein contains six putative transmembrane domains. Sequence comparison revealed that two yeast genes, FEN1 and JO343, shared significant similarities with SUR4. Mutants for SUR4 and FEN1 have the same pleiotropic phenotype, including bud localization defects, resistance to an immunosuppressor and resistance to ergosterol biosynthesis inhibitors. The double inactivation of SUR4 and FEN1 genes is lethal. These data and other aspects implicating SUR4 in glucose metabolism, suggest an involvement of these genes in the dynamics of cortical actin cytoskeleton in response to nutrient availability. Moreover, the existence of a fourth homologous gene in C. elegans extends the family to pluricellular organisms.

Published
1995

19. Yeast mutants affected in viability upon starvation have a modified phospholipid composition

Author

M. Bonneu, Michel Aigle, H. Juguelin, L. Desfarges, C. Cassagne, and Pascal Durrens

Subjects
Mutant, Saccharomyces cerevisiae, Genes, Fungal, Phospholipid, Bioengineering, Biology, medicine.disease_cause, Applied Microbiology and Biotechnology, Biochemistry, Biological pathway, chemistry.chemical_compound, Suppression, Genetic, Genetics, medicine, Gene, Crosses, Genetic, Phospholipids, Mutation, Genetic Complementation Test, biology.organism_classification, Yeast, Complementation, Phenotype, chemistry, Cell Division, Biotechnology
Abstract

Selection of mutations, based on the suppression of rvs161 delta defects, was performed. Ten mutants were obtained, ranged amongst four complementation groups, named SUR1, SUR2, SUR3 and SUR4. All sur mutations also suppress a mutation in another gene, RVS167, indicating that all six genes are involved in the same biological pathway. The sur mutant cells have abnormal morphologies in stationary phase, i.e. dumbbell-like in sur1, sur2 or sur3 strains and multi-budded in sur4 strains. Several phenotypic characteristics of the physiological suppressors as well as the rvs161 delta strain itself led us to analyse the phospholipid composition of the mutants. The assays show an overall decrease of the phospholipid amounts and modifications in the relative contents of some phospholipid classes in sur mutant cells.

Published
1993

20. The yeast ATP synthase subunit 4: structure and function

Author

Pascal Durrens, Monique Galante, Geneviève Arselin, Bernard Guerin, Jean Velours, Marie-Françoise Paul, and Michel Aigle

Subjects
Protein subunit, Specificity factor, Molecular Sequence Data, Gi alpha subunit, Saccharomyces cerevisiae, Biochemistry, Gamma-aminobutyric acid receptor subunit alpha-1, Electron Transport Complex IV, Structure-Activity Relationship, ATP synthase gamma subunit, Escherichia coli, Animals, Eukaryotic Small Ribosomal Subunit, Amino Acid Sequence, Base Sequence, ATP synthase, biology, Eukaryotic Large Ribosomal Subunit, General Medicine, Molecular biology, Mitochondria, Proton-Translocating ATPases, Phenotype, Mutation, biology.protein, Nucleic Acid Conformation, Cattle, Oligonucleotide Probes
Abstract

The structure of ATP synthase subunit 4 was determined by using the oligonucleotide probe procedure. This subunit is the fourth polypeptide of the complex when classifying subunits in order of decreasing molecular mass. Its relative molecular mass is 25 kDa. The ATP4 gene was isolated and sequenced. The nucleotide sequence predicts that subunit 4 is probably derived from a precursor protein 244 amino acids long. Mature subunit 4 contains 209 amino acid residues and the predicted molecular mass is 23250 kDa. Subunit 4 shows homology with the b-subunit of Escherichia coli ATP synthase and the b-subunit of beef heart mitochondrial ATP synthase. By using homologous transformation, a mutant lacking wild subunit 4 was constructed. This mutant is devoid of oxidative phosphorylation and F1 is loosely bound to the membrane. Our data are in favor of a structural relationship between subunit 4 and the mitochondrially-translated subunit 6 during biogenesis of F0.

Published
1989
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21. ATP4, the structural gene for yeast F0F1 ATPase subunit 4

Author

Michel Aigle, Jean Velours, Bernard Guerin, and Pascal Durrens

Subjects
Base Sequence, biology, Macromolecular Substances, Eukaryotic Large Ribosomal Subunit, Specificity factor, Protein subunit, Genes, Fungal, Molecular Sequence Data, DNA Restriction Enzymes, Saccharomyces cerevisiae, Biochemistry, Gamma-aminobutyric acid receptor subunit alpha-1, Molecular biology, Proton-Translocating ATPases, SCN3A, Genes, ATP synthase gamma subunit, Sequence Homology, Nucleic Acid, Escherichia coli, biology.protein, Genomic library, Eukaryotic Small Ribosomal Subunit, Amino Acid Sequence, Cloning, Molecular
Abstract

A plasmid containing the gene coding for the Saccharomyces cerevisiae F0F1 ATPase subunit 4 was isolated from a yeast genomic DNA library using the oligonucleotide probe procedure. The gene and the surrounding regions were cloned into M13 tg 130 and M13 tg 131 phage vectors. A 732-base-pair open reading frame encoding a 244-amino-acid polypeptide is described. The nucleotide sequence predicts that subunit 4 is probably derived from a precursor protein with a hydrophilic and basic 35-amino-acid leader sequence. Mature subunit 4 contains 209 amino acid residues and the predicted molecular mass is 23250 Da. This subunit presents amphiphilic behaviour with two distinct domains. A high alpha-helix content of 77% was predicted from the sequence. Subunit 4 shows homology with the b subunit of Escherichia coli ATP synthase.

Published
1988
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22. Genomic Exploration of the Hemiascomycetous Yeasts: 19. Ascomycetes-specific genes

Author

Claire Toffano-Nioche, Bertrand Llorente, Andrée Lépingle, Jacky de Montigny, Philippe Brottier, Elisabeth Bon, François Artiguenave, Bernard Dujon, Jean-Luc Souciet, Gaëlle Blandin, Alain Malpertuy, William Saurin, Pascal Durrens, Cécile Neuvéglise, Micheline Wésolowski-Louvel, Serge Potier, Claude Gaillardin, Serge Casaregola, Odile Ozier-Kalogeropoulos, Michel Aigle, Monique Bolotin-Fukuhara, Fredj Tekaia, Patrick Wincker, and Jean Weissenbach

Subjects
Maverick, Novel gene, Saccharomyces cerevisiae, Genes, Fungal, Biophysics, Questionable open reading frame, Biochemistry, Genome, Evolution, Molecular, Orphan, Ascomycota, Species Specificity, Structural Biology, Sequence comparison, Genetics, Gene number, ORFS, Molecular Biology, Gene, Conserved Sequence, biology, Base Sequence, Phylum, Genetic Variation, Cell Biology, biology.organism_classification, Yeast, Open reading frame
Abstract

Comparisons of the 6213 predicted Saccharomyces cerevisiae open reading frame (ORF) products with sequences from organisms of other biological phyla differentiate genes commonly conserved in evolution from ‘maverick’ genes which have no homologue in phyla other than the Ascomycetes. We show that a majority of the ‘maverick’ genes have homologues among other yeast species and thus define a set of 1892 genes that, from sequence comparisons, appear ‘Ascomycetes-specific’. We estimate, retrospectively, that the S. cerevisiae genome contains 5651 actual protein-coding genes, 50 of which were identified for the first time in this work, and that the present public databases contain 612 predicted ORFs that are not real genes. Interestingly, the sequences of the ‘Ascomycetes-specific’ genes tend to diverge more rapidly in evolution than that of other genes. Half of the ‘Ascomycetes-specific’ genes are functionally characterized in S. cerevisiae, and a few functional categories are over-represented in them.

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23. Genomic Exploration of the Hemiascomycetous Yeasts: 20. Evolution of gene redundancy compared to Saccharomyces cerevisiae

Author

William Saurin, Cécile Neuvéglise, Bertrand Llorente, Philippe Brottier, Andrée Lépingle, Bernard Dujon, Micheline Wésolowski-Louvel, Serge Casaregola, Monique Bolotin-Fukuhara, Claire Toffano-Nioche, Gaëlle Blandin, Elisabeth Bon, Odile Ozier-Kalogeropoulos, Patrick Wincker, Jean Weissenbach, Alain Malpertuy, François Artiguenave, Pascal Durrens, Michel Aigle, Serge Potier, Claude Gaillardin, Jean-Luc Souciet, Fredj Tekaia, Jacky de Montigny, Microbiologie et Génétique Moléculaire (MGM), and Institut National de la Recherche Agronomique (INRA)-Institut National Agronomique Paris-Grignon (INA P-G)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Genome evolution, Gene duplication, Genes, Fungal, Saccharomyces cerevisiae, Biophysics, Gene redundancy, [SDV.BC]Life Sciences [q-bio]/Cellular Biology, Biochemistry, Genome, Evolution, Molecular, 03 medical and health sciences, Ascomycota, Structural Biology, Gene cluster, Genetics, Gene family, Molecular Biology, Gene, Conserved Sequence, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, 0303 health sciences, Base Sequence, Models, Genetic, biology, Gene deletion, 030302 biochemistry & molecular biology, Genetic Variation, Cell Biology, Telomere, biology.organism_classification, Paralogue, Multigene Family, Orthologue, Genome, Fungal
Abstract

We have evaluated the degree of gene redundancy in the nuclear genomes of 13 hemiascomycetous yeast species. Saccharomyces cerevisiae singletons and gene families appear generally conserved in these species as singletons and families of similar size, respectively. Variations of the number of homologues with respect to that expected affect from 7 to less than 24% of each genome. Since S. cerevisiae homologues represent the majority of the genes identified in the genomes studied, the overall degree of gene redundancy seems conserved across all species. This is best explained by a dynamic equilibrium resulting from numerous events of gene duplication and deletion rather than by a massive duplication event occurring in some lineages and not in others.

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